betabandido, I guess you use Ambiance Ubuntu Gnome theme and Skype by default 
uses KDE theme.
So, to solve your issue with Skype go to Skype's "Options->General" and select 
"GTK+" style  in "Choose style" dropdown menu.

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Notification area icon wrongly rendered/uses bg_color as a background (multiple 
apps)
https://bugs.launchpad.net/bugs/403135
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